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Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with propranolol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 1.5 M sodium potassium phosphate pH 5.6, 3% MPD, soaking 150mM Propranolol, cryoprotected with 25% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.027 α = 90 b = 57.876 β = 110.09 c = 60.893 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Kb mirrors 2015-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.08 47.92 90 0.057 0.023 14.9 6.6 127862
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.08 1.1 86.3 0.604 2 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5OXU 1.08 47.92 121507 6330 89.78 0.15869 0.15848 0.1692 0.16266 0.1731 RANDOM 14.686
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.4 0.49 -0.77 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.004 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 12.296 r_rigid_bond_restr 11.566 r_dihedral_angle_1_deg 5.678 r_long_range_B_refined 4.142 r_long_range_B_other 4.141 r_sphericity_bonded 2.756 r_angle_refined_deg 1.429 r_scangle_other 1.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.004 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 12.296 r_rigid_bond_restr 11.566 r_dihedral_angle_1_deg 5.678 r_long_range_B_refined 4.142 r_long_range_B_other 4.141 r_sphericity_bonded 2.756 r_angle_refined_deg 1.429 r_scangle_other 1.234 r_angle_other_deg 0.998 r_mcangle_it 0.902 r_mcangle_other 0.902 r_scbond_other 0.736 r_scbond_it 0.735 r_mcbond_it 0.514 r_mcbond_other 0.514 r_chiral_restr 0.084 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2515 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing